Team:Dalhousie Halifax NS/Description
A “Spike” in Biofuel Production: Mining the Porcupine Microbiome to Engineer a Softwood Feedstock Platform
Dwindling fuel resources and rising environmental concerns have catalyzed the development of biofuel production in microorganisms. In Nova Scotia, softwood waste from the lumber industry is an untapped source for low-cost biofuel feedstock; however, this waste cannot be utilized by traditional biofuel processes due to toxic compounds such as turpentines and unavailable carbon compounds such as cellulose. The porcupine microbiome provides a unique solution as it is capable of digesting bark and toxic products. Working with Schubenacadie Wildlife Park, we aim to not only identify cellulose and/or turpentine-degrading bacteria in the porcupine microbiome, but to also characterize microbial communities found within the Park’s mammal population. To achieve these goals, we are using fecal samples to construct a DNA library of the porcupine and to analyze each mammal’s microbial rRNA. Future experiments include introducing identified cellulose and/or turpentine-degrading pathways into E. coli to produce an economically viable and sustainable biofuel-generating organism.
Shubenacadie Wildlife Park Microbiome Survey
The original thought was that since porcupines eat so much tree sap and bark/wood, their microbiome must be full of organisms capable of utilizing and breaking down these compounds. However, we had an opportunity to study close to the entire microbial community within the guts of the Shubenacadie mammals, so we took it! The entire survey of the park's microbiomes was incredibly helpful in the search for enzymes that could be utilized in cellulose breakdown, tree resin antimicrobial survival and biofuel production.
This survey was done by collecting fecal samples from 21 of the mammals found in the Shubenacadie Wildlife Park. The environmental DNA in these samples was extracted using the PowerFECAL kit from Mo Bio. This DNA was then put through 16S sequencing at the Integrated Microbiome Resource at Dalhousie University. This process involves the use of primers that target the constant regions of the 16S ribosomal RNA gene and amplify a roughly 500 basepair region that includes the variable region of the gene. This variable region is used to identify species. This amplified DNA is then seqeunced using Illumina MiSeq, and the sequence files are analyzed using the IMR's Microbiome Helper tool. This tool wraps many different software programs, including PEAR, VSEARCH and qiime. The data can then be visualized using pie, area, and bar charts, as well as beta-diversity plots.
Dr. Morgan Langille of the IMR at Dalhousie has also developed a software tool called piCRUST. This tool allows the use of 16S data to predict metagenome content and to also predict the enzymatic pathways and function of different species in a microbiome. This tool proved invaluable for us, and allowed us to find many important enzymes.
This will be a description of the second part of our project (isolation of cellulose and tree sap degrading bacteria from fecal samples)
This will be a description of the third part of out project (metagenomic library based on cells that degrade cellulose and sap)
